平行坐标图

作者

[编辑] 郑虎;

[审核] .

注记

Hiplot 网站

本页面为 Hiplot Parallel Coordinate 插件的源码版本教程，您也可以使用 Hiplot 网站实现无代码绘图，更多信息请查看以下链接:

https://hiplot.cn/basic/parallel-coordinate?lang=zh_cn

环境配置

  • 系统: Cross-platform (Linux/MacOS/Windows)

  • 编程语言: R

  • 依赖包: GGally; hrbrthemes; viridis; ggthemes

# 安装包
if (!requireNamespace("GGally", quietly = TRUE)) {
  install.packages("GGally")
}
if (!requireNamespace("hrbrthemes", quietly = TRUE)) {
  install.packages("hrbrthemes")
}
if (!requireNamespace("viridis", quietly = TRUE)) {
  install.packages("viridis")
}
if (!requireNamespace("ggthemes", quietly = TRUE)) {
  install.packages("ggthemes")
}

# 加载包
library(GGally)
library(hrbrthemes)
library(viridis)
library(ggthemes)

数据准备

# 加载数据
data <- read.delim("files/Hiplot/132-parallel-coordinate-data.txt", header = T)

# 整理数据格式
data[, 6] <- factor(data[, 6], levels = unique(data[, 6]))

# 查看数据
head(data)
    Name Value1 Value2 Value3 Value4       Group
1    ATR    5.1    3.5    1.4    0.2 p53 pathway
2  CHEK1    4.9    3.0    1.4    0.2 p53 pathway
3  GORAB    4.7    3.2    1.3    0.2 p53 pathway
4 CDKN2A    4.6    3.1    1.5    0.2 p53 pathway
5   MDM2    5.0    3.6    1.4    0.2 p53 pathway
6   MDM4    5.4    3.9    1.7    0.4 p53 pathway

可视化

# 平行坐标图
p <- ggparcoord(data, columns = 2:(ncol(data) - 1), groupColumn = ncol(data),
                title = "Parallel Coordinate Plot for cancer Data",
                alphaLines = 0.3, scale = "globalminmax",
                showPoints = T, boxplot = F) +
  theme_base() +
  theme(text = element_text(family = "Arial"),
        plot.title = element_text(size = 12, hjust = 0.5),
        axis.title = element_text(size = 10),
        axis.text = element_text(size = 12),
        axis.text.x = element_text(angle = 0, hjust = 0.5,vjust = 1),
        legend.position = "right",
        legend.direction = "vertical",
        legend.title = element_text(size = 10),
        legend.text = element_text(size = 10)) +
  scale_color_viridis(discrete = TRUE) +
  facet_grid(formula(paste("~", (colnames(data)[ncol(data)]))))

p
图 1: 平行坐标图